Multiple sequence alignment - TraesCS1B01G181500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G181500 chr1B 100.000 4739 0 0 615 5353 328435852 328440590 0.000000e+00 8752.0
1 TraesCS1B01G181500 chr1B 100.000 79 0 0 1 79 328435238 328435316 4.320000e-31 147.0
2 TraesCS1B01G181500 chr1D 94.219 4307 173 29 1031 5292 229065655 229069930 0.000000e+00 6505.0
3 TraesCS1B01G181500 chr1D 91.228 57 2 2 615 669 229065213 229065268 2.070000e-09 75.0
4 TraesCS1B01G181500 chr1A 92.750 2607 113 21 2719 5292 297379105 297381668 0.000000e+00 3698.0
5 TraesCS1B01G181500 chr1A 93.202 2133 84 33 615 2722 297376736 297378832 0.000000e+00 3079.0
6 TraesCS1B01G181500 chr1A 94.444 36 2 0 4787 4822 480572368 480572333 7.490000e-04 56.5
7 TraesCS1B01G181500 chr2A 88.136 118 12 2 5127 5243 88981291 88981175 7.230000e-29 139.0
8 TraesCS1B01G181500 chr2A 84.348 115 13 3 5130 5243 529556938 529557048 2.040000e-19 108.0
9 TraesCS1B01G181500 chr7D 94.030 67 4 0 5132 5198 628084434 628084500 9.490000e-18 102.0
10 TraesCS1B01G181500 chr7D 93.846 65 4 0 5132 5196 628003127 628003191 1.230000e-16 99.0
11 TraesCS1B01G181500 chr3A 90.541 74 7 0 5125 5198 127307437 127307510 1.230000e-16 99.0
12 TraesCS1B01G181500 chr3A 85.542 83 11 1 5130 5211 725478551 725478633 9.550000e-13 86.1
13 TraesCS1B01G181500 chr3D 89.706 68 7 0 5131 5198 98140948 98140881 2.660000e-13 87.9
14 TraesCS1B01G181500 chr4A 90.566 53 3 2 5302 5353 614166366 614166315 9.620000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G181500 chr1B 328435238 328440590 5352 False 4449.5 8752 100.0000 1 5353 2 chr1B.!!$F1 5352
1 TraesCS1B01G181500 chr1D 229065213 229069930 4717 False 3290.0 6505 92.7235 615 5292 2 chr1D.!!$F1 4677
2 TraesCS1B01G181500 chr1A 297376736 297381668 4932 False 3388.5 3698 92.9760 615 5292 2 chr1A.!!$F1 4677

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
29 30 0.249073 CGCGGATCGAGTCTGGATTT 60.249 55.0 0.00 0.00 41.67 2.17 F
49 50 0.249280 TTTGAAGCAGAGACACGCGA 60.249 50.0 15.93 0.00 0.00 5.87 F
1693 1734 0.392729 AGTACTACGAGTGGAGCGCT 60.393 55.0 11.27 11.27 0.00 5.92 F
2800 3126 0.034283 TGCCATTGCTGCATGACCTA 60.034 50.0 1.84 0.00 38.71 3.08 F
3703 4053 0.264359 AGAGAGGGAGGTGCTAGCAT 59.736 55.0 22.51 5.42 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1647 0.168788 CATGGTGCCACGTGTCATTC 59.831 55.000 15.65 5.42 0.00 2.67 R
1906 1948 2.809665 GCTCCAGAAGTCCATGCCATAG 60.810 54.545 0.00 0.00 0.00 2.23 R
3526 3860 0.365186 GTTTGTTTGTGTGTGTGCGC 59.635 50.000 0.00 0.00 0.00 6.09 R
3852 4202 0.675083 CAAGCTTGCACCACCAATGA 59.325 50.000 14.65 0.00 0.00 2.57 R
5076 5443 0.811616 CATACCAGCTCCGTTGCTCC 60.812 60.000 0.00 0.00 41.98 4.70 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.124860 TCGCGGATCGAGTCTGGA 60.125 61.111 6.13 0.00 43.16 3.86
27 28 1.526225 TCGCGGATCGAGTCTGGAT 60.526 57.895 6.13 0.00 43.16 3.41
28 29 1.101635 TCGCGGATCGAGTCTGGATT 61.102 55.000 6.13 0.00 43.16 3.01
29 30 0.249073 CGCGGATCGAGTCTGGATTT 60.249 55.000 0.00 0.00 41.67 2.17
30 31 1.802880 CGCGGATCGAGTCTGGATTTT 60.803 52.381 0.00 0.00 41.67 1.82
31 32 2.280628 GCGGATCGAGTCTGGATTTTT 58.719 47.619 0.00 0.00 33.56 1.94
47 48 2.755836 TTTTTGAAGCAGAGACACGC 57.244 45.000 0.00 0.00 0.00 5.34
48 49 0.581529 TTTTGAAGCAGAGACACGCG 59.418 50.000 3.53 3.53 0.00 6.01
49 50 0.249280 TTTGAAGCAGAGACACGCGA 60.249 50.000 15.93 0.00 0.00 5.87
50 51 0.939577 TTGAAGCAGAGACACGCGAC 60.940 55.000 15.93 3.56 0.00 5.19
51 52 2.429236 AAGCAGAGACACGCGACG 60.429 61.111 15.93 5.81 0.00 5.12
52 53 2.781750 GAAGCAGAGACACGCGACGA 62.782 60.000 15.93 0.00 0.00 4.20
53 54 3.166630 GCAGAGACACGCGACGAC 61.167 66.667 15.93 3.61 0.00 4.34
54 55 2.502080 CAGAGACACGCGACGACC 60.502 66.667 15.93 0.00 0.00 4.79
55 56 2.668889 AGAGACACGCGACGACCT 60.669 61.111 15.93 6.40 0.00 3.85
56 57 2.502080 GAGACACGCGACGACCTG 60.502 66.667 15.93 0.68 0.00 4.00
57 58 3.948086 GAGACACGCGACGACCTGG 62.948 68.421 15.93 0.00 0.00 4.45
64 65 4.436998 CGACGACCTGGCCCTGAC 62.437 72.222 0.00 0.00 0.00 3.51
65 66 4.436998 GACGACCTGGCCCTGACG 62.437 72.222 0.00 6.08 0.00 4.35
834 850 2.345991 CGCCAAGGTTCCTTCGGA 59.654 61.111 17.68 0.00 0.00 4.55
844 860 2.420269 GGTTCCTTCGGATTCTTCTCCC 60.420 54.545 0.00 0.00 31.04 4.30
856 874 0.467290 CTTCTCCCTCTCCCTCTCCG 60.467 65.000 0.00 0.00 0.00 4.63
864 882 1.152839 CTCCCTCTCCGACCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
886 904 2.689034 CGGCCCCTTCCTCTTCCT 60.689 66.667 0.00 0.00 0.00 3.36
974 992 3.752167 GGGGACGGAGGAGGAGGA 61.752 72.222 0.00 0.00 0.00 3.71
975 993 2.442458 GGGACGGAGGAGGAGGAC 60.442 72.222 0.00 0.00 0.00 3.85
1110 1137 3.322466 CCCAAGGTGACGCTCCCT 61.322 66.667 0.00 0.00 0.00 4.20
1217 1244 3.106407 GCTCGCGTCACCTGTGTC 61.106 66.667 5.77 0.00 0.00 3.67
1226 1253 2.997897 ACCTGTGTCCCTCCGCTC 60.998 66.667 0.00 0.00 0.00 5.03
1227 1254 3.775654 CCTGTGTCCCTCCGCTCC 61.776 72.222 0.00 0.00 0.00 4.70
1268 1296 1.933247 ATTACTGCTCGCTGCTTCTC 58.067 50.000 0.00 0.00 43.37 2.87
1286 1314 1.518572 CCACTCGCACACCGGATAC 60.519 63.158 9.46 0.00 37.59 2.24
1311 1339 9.649167 ACGCTGAATAATTACAACTACTACTTT 57.351 29.630 0.00 0.00 0.00 2.66
1312 1340 9.901724 CGCTGAATAATTACAACTACTACTTTG 57.098 33.333 0.00 0.00 0.00 2.77
1397 1435 1.301293 CTGTGCTTCCCTCCCTTCC 59.699 63.158 0.00 0.00 0.00 3.46
1469 1507 4.479158 TCCTACCTTTGGCTTGTCAATTT 58.521 39.130 0.00 0.00 0.00 1.82
1567 1605 5.906113 TGTCTTAATCTGAGACTGAGACC 57.094 43.478 12.31 0.00 43.07 3.85
1586 1627 2.508716 ACCCTGCTCATCATGTTGATCT 59.491 45.455 6.92 0.00 34.28 2.75
1657 1698 2.161012 CAGCGTCGAGTACTTCAACCTA 59.839 50.000 0.00 0.00 0.00 3.08
1693 1734 0.392729 AGTACTACGAGTGGAGCGCT 60.393 55.000 11.27 11.27 0.00 5.92
1756 1797 1.888512 GTGGTTCAGTACTACGTCCCA 59.111 52.381 0.00 0.00 0.00 4.37
1827 1868 3.780294 AGGTCTGCACCAAGATAACCATA 59.220 43.478 0.00 0.00 46.68 2.74
1906 1948 1.239347 GCAGGAGTTTTGGTGAGGAC 58.761 55.000 0.00 0.00 0.00 3.85
2002 2044 1.795872 TCATTTAACTGCGACGTGGTG 59.204 47.619 0.00 0.00 0.00 4.17
2035 2077 2.793831 GCGACCTGGCCATTTGTAT 58.206 52.632 5.51 0.00 0.00 2.29
2314 2356 7.543947 AAAGAAAGAAAATTTGGCAGACAAG 57.456 32.000 0.00 0.00 40.82 3.16
2461 2511 6.601613 TGAAGTGTTTATGTTCAGTTTGACCT 59.398 34.615 0.00 0.00 0.00 3.85
2466 2516 1.388547 TGTTCAGTTTGACCTGTGGC 58.611 50.000 0.00 0.00 34.02 5.01
2512 2562 3.808174 AGTAAGCGTTGTTTCTCTGTTCC 59.192 43.478 0.00 0.00 0.00 3.62
2525 2575 5.228945 TCTCTGTTCCGAAATCCTTTCTT 57.771 39.130 0.00 0.00 37.52 2.52
2702 2752 4.130857 TCTTCATTTCAAGGTACGTTGCA 58.869 39.130 20.77 9.74 0.00 4.08
2729 3055 5.035443 GCATGTAAGACACTAACTAGACCG 58.965 45.833 0.00 0.00 0.00 4.79
2730 3056 5.392811 GCATGTAAGACACTAACTAGACCGT 60.393 44.000 0.00 0.00 0.00 4.83
2800 3126 0.034283 TGCCATTGCTGCATGACCTA 60.034 50.000 1.84 0.00 38.71 3.08
2836 3162 7.725844 TGCTAGTCACTAATCATCCTAGATTCA 59.274 37.037 0.00 0.00 38.97 2.57
2930 3262 4.116238 GGATGTTCTCTCCTGATTTCGAC 58.884 47.826 0.00 0.00 0.00 4.20
3300 3633 3.251004 CCTTGGTGGAAGAAACTCGAAAG 59.749 47.826 0.00 0.00 38.35 2.62
3382 3716 7.485277 GTGTTCAGATACGTGGAGTATATATGC 59.515 40.741 0.00 0.00 45.47 3.14
3522 3856 2.899838 CCCCACCACACACACACG 60.900 66.667 0.00 0.00 0.00 4.49
3523 3857 3.582120 CCCACCACACACACACGC 61.582 66.667 0.00 0.00 0.00 5.34
3524 3858 3.935872 CCACCACACACACACGCG 61.936 66.667 3.53 3.53 0.00 6.01
3525 3859 4.589700 CACCACACACACACGCGC 62.590 66.667 5.73 0.00 0.00 6.86
3547 3897 2.257894 CGCACACACACAAACAAACAT 58.742 42.857 0.00 0.00 0.00 2.71
3610 3960 5.836358 AGGGTTTGTTCAGCTTGGTATTTTA 59.164 36.000 0.00 0.00 0.00 1.52
3666 4016 4.330074 CCCGTGTCTTAGCTTTCAAGTATG 59.670 45.833 0.00 0.00 0.00 2.39
3689 4039 2.344950 AGACAATTGCTTGCGAGAGAG 58.655 47.619 4.70 0.00 35.69 3.20
3703 4053 0.264359 AGAGAGGGAGGTGCTAGCAT 59.736 55.000 22.51 5.42 0.00 3.79
3852 4202 9.682465 GAAGGGTTCTTTCAGGTACTTATTATT 57.318 33.333 0.00 0.00 30.78 1.40
3854 4204 8.832735 AGGGTTCTTTCAGGTACTTATTATTCA 58.167 33.333 0.00 0.00 34.60 2.57
3985 4338 3.515602 ATTCTTTGAGCTTGACCCTGT 57.484 42.857 0.00 0.00 0.00 4.00
4032 4385 2.092375 AGTCCTTAATAACAGCTGCCCC 60.092 50.000 15.27 0.00 0.00 5.80
4092 4445 8.553459 ACTAGCTGTATTGATGGCATTATTAC 57.447 34.615 14.06 14.06 0.00 1.89
4199 4553 0.673644 CACTAGCCCCGTTTGGACTG 60.674 60.000 0.00 0.00 37.49 3.51
4217 4571 3.221771 ACTGGCAGCAAACAAGATACAA 58.778 40.909 15.89 0.00 0.00 2.41
4252 4606 0.419459 AACCCCAGGACAGGAGATCT 59.581 55.000 0.00 0.00 0.00 2.75
4295 4649 2.125188 GCAGCAGACTCCTGGCTC 60.125 66.667 0.00 0.00 40.72 4.70
4367 4721 4.949856 CCCATGTGAAGTACTAATTTGCCT 59.050 41.667 0.00 0.00 0.00 4.75
4368 4722 5.163622 CCCATGTGAAGTACTAATTTGCCTG 60.164 44.000 0.00 0.00 0.00 4.85
4369 4723 5.163622 CCATGTGAAGTACTAATTTGCCTGG 60.164 44.000 0.00 0.00 0.00 4.45
4370 4724 3.756434 TGTGAAGTACTAATTTGCCTGGC 59.244 43.478 12.87 12.87 0.00 4.85
4372 4726 3.245087 TGAAGTACTAATTTGCCTGGCCA 60.245 43.478 17.53 4.71 0.00 5.36
4373 4727 3.669939 AGTACTAATTTGCCTGGCCAT 57.330 42.857 17.53 5.36 0.00 4.40
4374 4728 3.290710 AGTACTAATTTGCCTGGCCATG 58.709 45.455 17.53 4.20 0.00 3.66
4375 4729 2.530460 ACTAATTTGCCTGGCCATGA 57.470 45.000 17.53 0.30 0.00 3.07
4376 4730 2.818921 ACTAATTTGCCTGGCCATGAA 58.181 42.857 17.53 0.00 0.00 2.57
4377 4731 2.497273 ACTAATTTGCCTGGCCATGAAC 59.503 45.455 17.53 0.00 0.00 3.18
4378 4732 0.614812 AATTTGCCTGGCCATGAACC 59.385 50.000 17.53 0.00 0.00 3.62
4379 4733 0.252375 ATTTGCCTGGCCATGAACCT 60.252 50.000 17.53 0.00 0.00 3.50
4380 4734 0.899717 TTTGCCTGGCCATGAACCTC 60.900 55.000 17.53 0.00 0.00 3.85
4381 4735 2.079088 TTGCCTGGCCATGAACCTCA 62.079 55.000 17.53 0.00 0.00 3.86
4382 4736 1.076485 GCCTGGCCATGAACCTCAT 60.076 57.895 12.80 0.00 37.65 2.90
4408 4762 5.062308 GCAGTAGACTTGAAATCGTCGAAAT 59.938 40.000 0.00 0.00 35.38 2.17
4449 4803 1.463444 GACACAAACCATCTACCGTGC 59.537 52.381 0.00 0.00 0.00 5.34
4481 4835 7.384115 CCTCGTAAAAGTTGAGTCTAACATTCA 59.616 37.037 7.78 0.00 33.02 2.57
4610 4966 5.073428 TGGTACTAGTCTGATATCCAGCTG 58.927 45.833 6.78 6.78 42.62 4.24
4694 5054 1.357137 TGTGTGCCCAGGATGAACTA 58.643 50.000 0.00 0.00 39.69 2.24
4762 5122 3.743521 TCAGTTGGACCTGAATCAGTTG 58.256 45.455 9.63 0.00 38.49 3.16
4901 5265 1.334869 ACAACTTGCGCCAGAAGAAAG 59.665 47.619 16.40 7.68 0.00 2.62
4921 5285 8.205131 AGAAAGCATAAATTCAATTGCAATCC 57.795 30.769 13.38 0.00 37.56 3.01
4993 5360 7.948278 ATTTAGTTTCTTTCCCTCGATATCG 57.052 36.000 19.14 19.14 41.45 2.92
5048 5415 7.637631 TGCTATTATCCAGCACAAAATGTTA 57.362 32.000 0.00 0.00 43.90 2.41
5113 5484 7.575414 TGGTATGTTGTGACAGTTACATTTT 57.425 32.000 6.69 0.00 39.58 1.82
5117 5488 9.730420 GTATGTTGTGACAGTTACATTTTCTTT 57.270 29.630 6.69 0.00 39.58 2.52
5133 5504 9.088987 ACATTTTCTTTACATGTAACCCAATCT 57.911 29.630 17.85 0.62 29.07 2.40
5252 5630 4.312443 CGTGGTGGTACTATCTGTTTGTT 58.688 43.478 0.00 0.00 0.00 2.83
5258 5636 3.302699 GGTACTATCTGTTTGTTCGACGC 59.697 47.826 0.00 0.00 0.00 5.19
5265 5643 1.064803 TGTTTGTTCGACGCTGCATTT 59.935 42.857 0.00 0.00 0.00 2.32
5277 5655 4.309099 ACGCTGCATTTGATTTTCATGTT 58.691 34.783 0.00 0.00 0.00 2.71
5278 5656 4.150980 ACGCTGCATTTGATTTTCATGTTG 59.849 37.500 0.00 0.00 0.00 3.33
5280 5658 4.670735 GCTGCATTTGATTTTCATGTTGGC 60.671 41.667 0.00 0.00 0.00 4.52
5288 5666 1.255882 TTTCATGTTGGCGGCTTGAT 58.744 45.000 11.43 0.00 0.00 2.57
5292 5670 0.255890 ATGTTGGCGGCTTGATAGGT 59.744 50.000 11.43 0.00 0.00 3.08
5293 5671 0.676466 TGTTGGCGGCTTGATAGGTG 60.676 55.000 11.43 0.00 0.00 4.00
5294 5672 1.077787 TTGGCGGCTTGATAGGTGG 60.078 57.895 11.43 0.00 0.00 4.61
5295 5673 2.203209 GGCGGCTTGATAGGTGGG 60.203 66.667 0.00 0.00 0.00 4.61
5296 5674 2.742116 GGCGGCTTGATAGGTGGGA 61.742 63.158 0.00 0.00 0.00 4.37
5297 5675 1.227674 GCGGCTTGATAGGTGGGAG 60.228 63.158 0.00 0.00 0.00 4.30
5298 5676 1.227674 CGGCTTGATAGGTGGGAGC 60.228 63.158 0.00 0.00 0.00 4.70
5299 5677 1.690219 CGGCTTGATAGGTGGGAGCT 61.690 60.000 0.00 0.00 33.96 4.09
5300 5678 0.107643 GGCTTGATAGGTGGGAGCTC 59.892 60.000 4.71 4.71 33.96 4.09
5301 5679 0.107643 GCTTGATAGGTGGGAGCTCC 59.892 60.000 25.59 25.59 0.00 4.70
5302 5680 1.799933 CTTGATAGGTGGGAGCTCCT 58.200 55.000 31.36 14.95 37.80 3.69
5303 5681 2.964209 CTTGATAGGTGGGAGCTCCTA 58.036 52.381 31.36 24.44 40.07 2.94
5304 5682 3.515562 CTTGATAGGTGGGAGCTCCTAT 58.484 50.000 31.36 20.62 46.03 2.57
5305 5683 4.678256 CTTGATAGGTGGGAGCTCCTATA 58.322 47.826 31.36 16.62 44.18 1.31
5306 5684 4.323569 TGATAGGTGGGAGCTCCTATAG 57.676 50.000 31.36 0.00 44.18 1.31
5307 5685 3.011821 TGATAGGTGGGAGCTCCTATAGG 59.988 52.174 31.36 13.07 44.18 2.57
5308 5686 1.547099 AGGTGGGAGCTCCTATAGGA 58.453 55.000 31.36 20.53 43.08 2.94
5309 5687 1.866943 AGGTGGGAGCTCCTATAGGAA 59.133 52.381 31.36 3.71 44.91 3.36
5310 5688 2.158234 AGGTGGGAGCTCCTATAGGAAG 60.158 54.545 31.36 16.12 44.91 3.46
5311 5689 1.621317 GTGGGAGCTCCTATAGGAAGC 59.379 57.143 31.36 23.47 44.91 3.86
5312 5690 1.220493 TGGGAGCTCCTATAGGAAGCA 59.780 52.381 31.36 14.97 44.91 3.91
5313 5691 2.158097 TGGGAGCTCCTATAGGAAGCAT 60.158 50.000 31.36 20.26 44.91 3.79
5314 5692 2.909662 GGGAGCTCCTATAGGAAGCATT 59.090 50.000 31.36 18.22 44.91 3.56
5315 5693 3.055458 GGGAGCTCCTATAGGAAGCATTC 60.055 52.174 31.36 22.55 44.91 2.67
5316 5694 3.837731 GGAGCTCCTATAGGAAGCATTCT 59.162 47.826 29.32 17.49 46.56 2.40
5317 5695 4.322650 GGAGCTCCTATAGGAAGCATTCTG 60.323 50.000 29.32 16.51 46.56 3.02
5318 5696 3.007831 AGCTCCTATAGGAAGCATTCTGC 59.992 47.826 29.32 22.81 46.56 4.26
5319 5697 3.583806 CTCCTATAGGAAGCATTCTGCG 58.416 50.000 21.93 3.17 46.56 5.18
5320 5698 2.965831 TCCTATAGGAAGCATTCTGCGT 59.034 45.455 19.59 0.00 46.56 5.24
5327 5705 4.983090 GCATTCTGCGTCGAATGG 57.017 55.556 21.79 10.22 46.47 3.16
5328 5706 2.383170 GCATTCTGCGTCGAATGGA 58.617 52.632 21.79 0.00 46.47 3.41
5329 5707 0.302890 GCATTCTGCGTCGAATGGAG 59.697 55.000 21.79 1.55 46.47 3.86
5330 5708 0.302890 CATTCTGCGTCGAATGGAGC 59.697 55.000 16.25 0.00 44.02 4.70
5331 5709 1.148157 ATTCTGCGTCGAATGGAGCG 61.148 55.000 0.00 0.00 32.64 5.03
5332 5710 3.918220 CTGCGTCGAATGGAGCGC 61.918 66.667 0.00 0.00 41.96 5.92
5350 5728 4.541482 GCGCCGCACATGGTGATG 62.541 66.667 3.15 0.00 42.25 3.07
5351 5729 4.541482 CGCCGCACATGGTGATGC 62.541 66.667 0.00 0.00 42.25 3.91
5352 5730 3.442167 GCCGCACATGGTGATGCA 61.442 61.111 6.80 0.00 42.17 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.752796 TCGATCCGCGATCCTTTTT 57.247 47.368 8.23 0.00 45.59 1.94
10 11 0.249073 AAATCCAGACTCGATCCGCG 60.249 55.000 0.00 0.00 42.69 6.46
11 12 1.941325 AAAATCCAGACTCGATCCGC 58.059 50.000 0.00 0.00 0.00 5.54
28 29 1.003972 CGCGTGTCTCTGCTTCAAAAA 60.004 47.619 0.00 0.00 0.00 1.94
29 30 0.581529 CGCGTGTCTCTGCTTCAAAA 59.418 50.000 0.00 0.00 0.00 2.44
30 31 0.249280 TCGCGTGTCTCTGCTTCAAA 60.249 50.000 5.77 0.00 0.00 2.69
31 32 0.939577 GTCGCGTGTCTCTGCTTCAA 60.940 55.000 5.77 0.00 0.00 2.69
32 33 1.371758 GTCGCGTGTCTCTGCTTCA 60.372 57.895 5.77 0.00 0.00 3.02
33 34 2.429351 CGTCGCGTGTCTCTGCTTC 61.429 63.158 5.77 0.00 0.00 3.86
34 35 2.429236 CGTCGCGTGTCTCTGCTT 60.429 61.111 5.77 0.00 0.00 3.91
35 36 3.354645 TCGTCGCGTGTCTCTGCT 61.355 61.111 5.77 0.00 0.00 4.24
36 37 3.166630 GTCGTCGCGTGTCTCTGC 61.167 66.667 5.77 0.00 0.00 4.26
37 38 2.502080 GGTCGTCGCGTGTCTCTG 60.502 66.667 5.77 0.00 0.00 3.35
38 39 2.668889 AGGTCGTCGCGTGTCTCT 60.669 61.111 5.77 0.00 0.00 3.10
39 40 2.502080 CAGGTCGTCGCGTGTCTC 60.502 66.667 5.77 0.00 0.00 3.36
40 41 4.039357 CCAGGTCGTCGCGTGTCT 62.039 66.667 5.77 0.39 0.00 3.41
47 48 4.436998 GTCAGGGCCAGGTCGTCG 62.437 72.222 6.18 0.00 0.00 5.12
48 49 4.436998 CGTCAGGGCCAGGTCGTC 62.437 72.222 6.18 0.00 0.00 4.20
709 718 4.179599 GGAGGAGAGGGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
714 723 1.934459 ATTCGTCGGAGGAGAGGGGA 61.934 60.000 0.31 0.00 0.00 4.81
717 726 2.544069 GCTTTATTCGTCGGAGGAGAGG 60.544 54.545 0.31 0.00 0.00 3.69
719 728 1.407979 GGCTTTATTCGTCGGAGGAGA 59.592 52.381 0.31 0.00 0.00 3.71
720 729 1.136305 TGGCTTTATTCGTCGGAGGAG 59.864 52.381 0.31 0.00 0.00 3.69
721 730 1.134907 GTGGCTTTATTCGTCGGAGGA 60.135 52.381 0.00 0.00 0.00 3.71
834 850 2.090775 GGAGAGGGAGAGGGAGAAGAAT 60.091 54.545 0.00 0.00 0.00 2.40
844 860 0.179029 GAGAGGTCGGAGAGGGAGAG 60.179 65.000 0.00 0.00 36.95 3.20
856 874 3.844090 GGCCGAGCAGGAGAGGTC 61.844 72.222 2.12 0.00 45.00 3.85
864 882 4.168291 GAGGAAGGGGCCGAGCAG 62.168 72.222 0.00 0.00 0.00 4.24
874 892 1.681486 GCTCCCGAGGAAGAGGAAGG 61.681 65.000 0.00 0.00 0.00 3.46
957 975 3.752167 TCCTCCTCCTCCGTCCCC 61.752 72.222 0.00 0.00 0.00 4.81
958 976 2.442458 GTCCTCCTCCTCCGTCCC 60.442 72.222 0.00 0.00 0.00 4.46
959 977 2.829458 CGTCCTCCTCCTCCGTCC 60.829 72.222 0.00 0.00 0.00 4.79
960 978 1.820481 CTCGTCCTCCTCCTCCGTC 60.820 68.421 0.00 0.00 0.00 4.79
961 979 2.272797 CTCGTCCTCCTCCTCCGT 59.727 66.667 0.00 0.00 0.00 4.69
962 980 2.517402 CCTCGTCCTCCTCCTCCG 60.517 72.222 0.00 0.00 0.00 4.63
963 981 2.835895 GCCTCGTCCTCCTCCTCC 60.836 72.222 0.00 0.00 0.00 4.30
964 982 3.213402 CGCCTCGTCCTCCTCCTC 61.213 72.222 0.00 0.00 0.00 3.71
1110 1137 4.032452 GCGGGGTTTACGGGGGAA 62.032 66.667 0.00 0.00 0.00 3.97
1268 1296 1.518572 GTATCCGGTGTGCGAGTGG 60.519 63.158 0.00 0.00 0.00 4.00
1286 1314 9.901724 CAAAGTAGTAGTTGTAATTATTCAGCG 57.098 33.333 0.00 0.00 0.00 5.18
1310 1338 7.023171 AGGAACAAATATGTACTGGTACCAA 57.977 36.000 17.11 0.39 39.40 3.67
1311 1339 6.630203 AGGAACAAATATGTACTGGTACCA 57.370 37.500 15.39 15.39 39.40 3.25
1312 1340 6.882678 ACAAGGAACAAATATGTACTGGTACC 59.117 38.462 4.43 4.43 39.40 3.34
1314 1342 8.158132 TGAACAAGGAACAAATATGTACTGGTA 58.842 33.333 0.00 0.00 39.40 3.25
1315 1343 7.001674 TGAACAAGGAACAAATATGTACTGGT 58.998 34.615 0.00 0.00 39.40 4.00
1316 1344 7.447374 TGAACAAGGAACAAATATGTACTGG 57.553 36.000 0.00 0.00 39.40 4.00
1317 1345 9.912634 AAATGAACAAGGAACAAATATGTACTG 57.087 29.630 0.00 0.00 39.40 2.74
1397 1435 1.731433 CGCATCCCAATCAGGCAAGG 61.731 60.000 0.00 0.00 35.39 3.61
1535 1573 8.247562 AGTCTCAGATTAAGACATGACAAGTAC 58.752 37.037 0.00 0.00 44.54 2.73
1567 1605 4.989797 GTCTAGATCAACATGATGAGCAGG 59.010 45.833 21.24 13.50 37.20 4.85
1586 1627 2.252072 GACAGCCGGCCATTGGTCTA 62.252 60.000 26.15 0.00 0.00 2.59
1606 1647 0.168788 CATGGTGCCACGTGTCATTC 59.831 55.000 15.65 5.42 0.00 2.67
1693 1734 4.197498 GTAGCTCCGGCGCCGTAA 62.197 66.667 43.12 30.56 44.37 3.18
1756 1797 7.010771 TGTATAGCTGTATCCCTGACAAGTAT 58.989 38.462 0.00 0.00 0.00 2.12
1827 1868 9.252962 GAAATCAACATCAAGTCAAAATCAAGT 57.747 29.630 0.00 0.00 0.00 3.16
1842 1883 3.181483 GCCCACATCCAGAAATCAACATC 60.181 47.826 0.00 0.00 0.00 3.06
1906 1948 2.809665 GCTCCAGAAGTCCATGCCATAG 60.810 54.545 0.00 0.00 0.00 2.23
2035 2077 6.924111 AGAGCAAACTTCAAAGAACTCAAAA 58.076 32.000 0.00 0.00 0.00 2.44
2077 2119 7.663081 TCATAGAAATTCACCTTATCCATGAGC 59.337 37.037 0.00 0.00 0.00 4.26
2113 2155 4.208746 AGCACGACTAGGATAAGCTACTT 58.791 43.478 0.00 0.00 0.00 2.24
2301 2343 2.629137 TGTGATTGCTTGTCTGCCAAAT 59.371 40.909 0.00 0.00 31.20 2.32
2314 2356 6.672147 AGAAACTCTTATGTTGTGTGATTGC 58.328 36.000 0.00 0.00 0.00 3.56
2461 2511 1.065926 AGAAATGATGAGAGCGCCACA 60.066 47.619 2.29 1.87 0.00 4.17
2466 2516 4.202101 ACCTAGACAGAAATGATGAGAGCG 60.202 45.833 0.00 0.00 0.00 5.03
2525 2575 6.003326 TCACAGAGAACAAAATGAATAGCCA 58.997 36.000 0.00 0.00 0.00 4.75
2702 2752 7.091443 GTCTAGTTAGTGTCTTACATGCAACT 58.909 38.462 0.00 0.00 33.70 3.16
2729 3055 6.441093 TGTGCCATTAGAGATGATCAAAAC 57.559 37.500 0.00 0.00 0.00 2.43
2730 3056 6.885918 TCTTGTGCCATTAGAGATGATCAAAA 59.114 34.615 0.00 0.00 0.00 2.44
2800 3126 7.503549 TGATTAGTGACTAGCATCATTGTCAT 58.496 34.615 3.50 0.00 40.78 3.06
2836 3162 2.892852 CAACACAAATGGACATCACCCT 59.107 45.455 0.00 0.00 0.00 4.34
2930 3262 3.941483 CCAAGCACACTAACCCAATCTAG 59.059 47.826 0.00 0.00 0.00 2.43
2993 3325 5.163077 TGTTTATAAGAGTGGTTGGGGAACA 60.163 40.000 0.00 0.00 0.00 3.18
2994 3326 5.318630 TGTTTATAAGAGTGGTTGGGGAAC 58.681 41.667 0.00 0.00 0.00 3.62
3197 3529 3.409570 GAAAGGTTTCCCCAGAGTACAC 58.590 50.000 0.00 0.00 34.66 2.90
3300 3633 6.174049 AGGTAATTGAGAAAGCTACAGTTCC 58.826 40.000 0.00 0.00 0.00 3.62
3523 3857 4.877882 TTTGTGTGTGTGCGCGCG 62.878 61.111 28.44 28.44 38.36 6.86
3524 3858 3.311752 GTTTGTGTGTGTGCGCGC 61.312 61.111 27.26 27.26 36.27 6.86
3525 3859 1.067743 TTTGTTTGTGTGTGTGCGCG 61.068 50.000 0.00 0.00 0.00 6.86
3526 3860 0.365186 GTTTGTTTGTGTGTGTGCGC 59.635 50.000 0.00 0.00 0.00 6.09
3527 3861 1.691127 TGTTTGTTTGTGTGTGTGCG 58.309 45.000 0.00 0.00 0.00 5.34
3528 3862 4.151335 TCAAATGTTTGTTTGTGTGTGTGC 59.849 37.500 5.48 0.00 39.50 4.57
3547 3897 4.655963 ACTCTTGGAAGCTAAGCATCAAA 58.344 39.130 0.00 0.00 0.00 2.69
3610 3960 5.053978 ACTGAAGATGAAGGTTTGGAAGT 57.946 39.130 0.00 0.00 0.00 3.01
3666 4016 3.679980 TCTCTCGCAAGCAATTGTCTAAC 59.320 43.478 7.40 0.74 37.18 2.34
3689 4039 2.426842 AGAAAATGCTAGCACCTCCC 57.573 50.000 22.07 8.62 0.00 4.30
3731 4081 4.081972 TCAAGCTATGTGACAAGAGAGTCC 60.082 45.833 2.41 0.00 37.73 3.85
3852 4202 0.675083 CAAGCTTGCACCACCAATGA 59.325 50.000 14.65 0.00 0.00 2.57
3940 4292 4.322049 GGCTTGTTTAGACTCTCTACTGCA 60.322 45.833 0.00 0.00 0.00 4.41
4032 4385 2.031420 CAGTGTTCAAGGCATGTCACTG 60.031 50.000 23.41 23.41 45.66 3.66
4199 4553 2.672195 GCCTTGTATCTTGTTTGCTGCC 60.672 50.000 0.00 0.00 0.00 4.85
4217 4571 1.484444 GGTTGGTCCACAGAGAGCCT 61.484 60.000 0.00 0.00 35.97 4.58
4295 4649 2.037136 CCGGACTCCAAGCTGCTTG 61.037 63.158 30.44 30.44 40.75 4.01
4354 4708 3.287222 TCATGGCCAGGCAAATTAGTAC 58.713 45.455 13.87 0.00 0.00 2.73
4372 4726 3.110705 AGTCTACTGCCATGAGGTTCAT 58.889 45.455 0.00 0.00 37.65 2.57
4373 4727 2.540383 AGTCTACTGCCATGAGGTTCA 58.460 47.619 0.00 0.00 37.19 3.18
4374 4728 3.055819 TCAAGTCTACTGCCATGAGGTTC 60.056 47.826 0.00 0.00 37.19 3.62
4375 4729 2.906389 TCAAGTCTACTGCCATGAGGTT 59.094 45.455 0.00 0.00 37.19 3.50
4376 4730 2.540383 TCAAGTCTACTGCCATGAGGT 58.460 47.619 0.00 0.00 37.19 3.85
4377 4731 3.616956 TTCAAGTCTACTGCCATGAGG 57.383 47.619 0.00 0.00 38.23 3.86
4378 4732 4.269603 CGATTTCAAGTCTACTGCCATGAG 59.730 45.833 0.00 0.00 0.00 2.90
4379 4733 4.183865 CGATTTCAAGTCTACTGCCATGA 58.816 43.478 0.00 0.00 0.00 3.07
4380 4734 3.935203 ACGATTTCAAGTCTACTGCCATG 59.065 43.478 0.00 0.00 0.00 3.66
4381 4735 4.184629 GACGATTTCAAGTCTACTGCCAT 58.815 43.478 0.00 0.00 34.74 4.40
4382 4736 3.585862 GACGATTTCAAGTCTACTGCCA 58.414 45.455 0.00 0.00 34.74 4.92
4383 4737 2.599082 CGACGATTTCAAGTCTACTGCC 59.401 50.000 0.00 0.00 35.38 4.85
4384 4738 3.499048 TCGACGATTTCAAGTCTACTGC 58.501 45.455 0.00 0.00 35.38 4.40
4385 4739 6.633668 ATTTCGACGATTTCAAGTCTACTG 57.366 37.500 0.00 0.00 35.38 2.74
4386 4740 6.401153 GCAATTTCGACGATTTCAAGTCTACT 60.401 38.462 0.00 0.00 35.38 2.57
4449 4803 2.343101 TCAACTTTTACGAGGGCGATG 58.657 47.619 0.00 0.00 41.64 3.84
4481 4835 4.595781 TCAAGCCGTATAAACCTATCCCAT 59.404 41.667 0.00 0.00 0.00 4.00
4610 4966 2.298729 ACAATATGCACCCAACCACAAC 59.701 45.455 0.00 0.00 0.00 3.32
4694 5054 4.096984 CAGAAAACAGGACTCTGCAAAAGT 59.903 41.667 1.17 1.17 44.59 2.66
4901 5265 5.557514 CGCTGGATTGCAATTGAATTTATGC 60.558 40.000 14.33 7.30 39.22 3.14
4921 5285 3.764810 TTTGTGTTTGCGGGCGCTG 62.765 57.895 7.64 0.67 42.51 5.18
4963 5327 7.848128 TCGAGGGAAAGAAACTAAATAGATGT 58.152 34.615 0.00 0.00 0.00 3.06
5048 5415 8.128582 CGTGTTGCCATAAGAATACAATATGTT 58.871 33.333 0.00 0.00 0.00 2.71
5076 5443 0.811616 CATACCAGCTCCGTTGCTCC 60.812 60.000 0.00 0.00 41.98 4.70
5153 5524 8.780846 TGGAGAAACGCATCTTACTTTATTAA 57.219 30.769 0.00 0.00 0.00 1.40
5154 5525 8.780846 TTGGAGAAACGCATCTTACTTTATTA 57.219 30.769 0.00 0.00 0.00 0.98
5188 5559 7.660030 AAGAAAACTAATATGGGTGAATGGG 57.340 36.000 0.00 0.00 0.00 4.00
5231 5609 4.387862 CGAACAAACAGATAGTACCACCAC 59.612 45.833 0.00 0.00 0.00 4.16
5232 5610 4.281435 TCGAACAAACAGATAGTACCACCA 59.719 41.667 0.00 0.00 0.00 4.17
5234 5612 4.322804 CGTCGAACAAACAGATAGTACCAC 59.677 45.833 0.00 0.00 0.00 4.16
5252 5630 2.225255 TGAAAATCAAATGCAGCGTCGA 59.775 40.909 0.00 0.00 0.00 4.20
5258 5636 4.434989 CGCCAACATGAAAATCAAATGCAG 60.435 41.667 0.00 0.00 0.00 4.41
5265 5643 1.255882 AGCCGCCAACATGAAAATCA 58.744 45.000 0.00 0.00 0.00 2.57
5277 5655 2.589540 CCACCTATCAAGCCGCCA 59.410 61.111 0.00 0.00 0.00 5.69
5278 5656 2.203209 CCCACCTATCAAGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
5280 5658 1.227674 GCTCCCACCTATCAAGCCG 60.228 63.158 0.00 0.00 0.00 5.52
5288 5666 2.727024 TCCTATAGGAGCTCCCACCTA 58.273 52.381 29.54 15.33 39.78 3.08
5292 5670 1.220493 TGCTTCCTATAGGAGCTCCCA 59.780 52.381 29.54 17.52 46.36 4.37
5293 5671 2.016905 TGCTTCCTATAGGAGCTCCC 57.983 55.000 29.54 11.59 46.36 4.30
5294 5672 3.837731 AGAATGCTTCCTATAGGAGCTCC 59.162 47.826 28.38 26.22 46.36 4.70
5295 5673 4.819769 CAGAATGCTTCCTATAGGAGCTC 58.180 47.826 28.38 22.28 46.36 4.09
5296 5674 4.888326 CAGAATGCTTCCTATAGGAGCT 57.112 45.455 28.38 17.78 46.36 4.09
5312 5690 1.148157 CGCTCCATTCGACGCAGAAT 61.148 55.000 0.71 0.71 41.12 2.40
5313 5691 1.805539 CGCTCCATTCGACGCAGAA 60.806 57.895 0.00 0.00 34.31 3.02
5314 5692 2.202610 CGCTCCATTCGACGCAGA 60.203 61.111 0.00 0.00 0.00 4.26
5333 5711 4.541482 CATCACCATGTGCGGCGC 62.541 66.667 27.44 27.44 32.98 6.53
5334 5712 4.541482 GCATCACCATGTGCGGCG 62.541 66.667 0.51 0.51 32.98 6.46
5335 5713 3.442167 TGCATCACCATGTGCGGC 61.442 61.111 0.00 0.00 44.11 6.53


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.